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We compared the trophic niches of freshwater sculpins Cottus spp. with those of other co‐habiting forage fishes in two groups of boreal lakes with distinct habitats and fish communities. Near North Lakes (45° 00′ to 47° 30′ N) were deeper, stratified and contained lake trout Salvelinus namaycush as the apex piscivore, whereas Far North Lakes (51° 10′ to 52° 20′ N) were shallower, did not stratify and contained pike Esox lucius and walleye Sander vitreus as the apex piscivores. Trophic niches of sculpins and other forage fishes were compared based on niche metrics calculated from muscle stable carbon (δ13C) and nitrogen (δ15N) isotope ratios. In Near North Lakes, sculpins were found almost exclusively in deep, offshore waters and their niche positions reflected a greater reliance on pelagic production (lower δ13C) and a higher trophic elevation (higher δ15N) compared with most other forage fishes. Furthermore, sculpins in Near North Lakes tended to have larger trophic niches (occupied greater area in δ13C– δ15N space), particularly in the food chain (δ15N) dimension, than other cohabiting forage fishes. In contrast, sculpins in Far North Lakes were commonly found in the nearshore and had trophic niche positions and sizes that were similar to those of the other cohabiting forage fishes. This study illustrates the flexibility in the realised trophic niches of sculpins in relation to habitat availability and fish community composition in boreal lakes. [ABSTRACT FROM AUTHOR]